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Structural Biology

How transcription gets its start, in pictures

After years of effort, 3 different research groups have astonished the field with high-resolution cryo-EM structures of the machinery that reads our DNA

by Laura Howes
August 4, 2021 | A version of this story appeared in Volume 99, Issue 29

Cryo-electron microscopy
structure of the human preinitiation complex.
Credit: Yuan He/Science
The human preinitiation complex has been a complicated puzzle for structural biologists to put together.

DNA, the long polymer curled up inside our cells, is often described as the instructions for life. But those instructions are stored in DNA’s chemical code, and reading that code requires the coordination of multiple pieces of biological machinery. This year, scientists finally captured complete atomic-level pictures of the human machinery that starts that process, transcription.

Stretches of DNA aren’t directly translated into the proteins they encode. They are first transcribed into RNA, and that requires an enzyme called RNA polymerase II. But that simple sentence belies the complicated mechanisms involved in the transcription process. RNA polymerase II, or Pol II, doesn’t start working on its own. Transcription factors first bind to the DNA, forming a complex that recruits Pol II, even more transcription factors, and a mediator complex that together stabilize the whole assembly. The result is the weighty preinitiation complex (PIC), consisting of about 75 different proteins.

For the past 20 years, researchers around the world have picked away at the problem of what the human PIC looks like and how it works. But getting to a clear structure of the entire complex was far from a given: it was considered too big, too floppy, too unstable.

Then, in early 2021, a flurry of papers appeared from three labs—one in the US, one in Germany, and one in China. Taken together, they tell the story of how this key piece of biological machinery assembles and how it starts the transcription process.

“It’s amazing to finally see this big puzzle of all these pieces fitting together,” says Alexis Verger, a molecular biologist at Lille University who was not involved in the studies. “It’s only one step, but I think we have a clear picture” of what the start of transcription looks like, he adds.

That insight isn’t just important for academic research. It’s crucial to understanding how genes are regulated in healthy cells and how that process goes awry in unhealthy ones—information that can suggest new approaches to treating diseases like cancer. “Rational design of compounds to disrupt key interfaces [in the PIC] is probably going on right now,” says Dylan Taatjes, whose lab at the University of Colorado Boulder studies transcription regulation. “That is a new frontier that has opened up because of these structural insights.”

To image the complex, you first have to make it. These new structures build on years of painstaking work by research teams that not only established methods for isolating all the PIC’s protein components in the lab but coaxed those pieces into assembling in just the right way, without the whole complex falling apart.

Once that complex was made, recent improvements in cryo-electron microscopy were key to imaging it, says Max Planck Institute of Physical Chemistry’s Patrick Cramer, who led one of the three teams that published the detailed studies of human transcription machinery (Nature 2021, DOI: 10.1038/s41586-021-03554-8 and 10.1038/s41586-021-03555-7).

View of the preinitiation complex structure from the Cramer lab with a shorter version of the mediator.
Credit: Patrick Cramer/Nature
Patrick Cramer's lab used a shorter version of the mediator (blue sections) to solve this structure of the preinitiation complex. The RNA polymerase II is light gray.

In the run-up to publishing the structures of the human PIC, Cramer’s lab and others produced high-resolution structures of the yeast version, which is smaller and less complex. Then, last year, a group of researchers led by Francisco Asturias at the University of Colorado Denver published a paper as a preprint showing the structure of a mouse mediator complex. The work has since been peer-reviewed (Nat. Commun. 2021, DOI: 10.1038/s41467-021-21601-w).

“As soon as we saw that paper, we were telling ourselves, ‘We have to get our papers out,’ ” recalls Northwestern University’s Yuan He, one of the group leaders who have recently released structures of the PIC (Science 2021, DOI: 10.1126/science.abg3074). “So that basically started a cascade.”

Each of the groups used a different method to produce and assemble the dozens of proteins in the PIC. Overall, the resulting structures are strikingly similar, though each structure contains a slightly distinct view. Researchers are poring over these details to understand how parts of the complex interact, come together, and change shape; how key parts can alter the stability of the complex; and how the RNA polymerase is finally released to start reading and transcribing the code hidden in the DNA. The more Pol II that is released, the more a gene is expressed.

The resolution of these structures is in a new realm.
Dylan Taatjes, professor, University of Colorado Boulder

Before researchers obtained a 3D view of this machinery, they had been able to figure out some of the PIC’s key functions and interactions using biochemical assays, He says. Those experimental findings now make complete sense. It’s one thing to know that a mutation changes the activity of the complex and another to be able to explain why that activity is altered because of where it is in the protein.

The new structures “certainly confirmed a number of things,” Taatjes says. “But then there are a lot of completely new understandings from a molecular level because the resolution of these structures is in a new realm.”

For Taatjes, one of the biggest insights came from the work of Fudan University’s Yanhui Xu (Science 2021, DOI: 10.1126/science.aba8490 and 10.1126/science.abg0635). His lab produced multiple structures of the mediator, both on its own and bound to the PIC, displaying various confirmations of the protein complex. The results suggest how the mediator, which relays biochemical messages into changes in gene expression, changes the shape of the PIC when it binds.

Credit: YanhuiXu/Science
The Xu lab managed to get different snapshots that suggest how the preinitiation complex rearranges as it comes together.

These snapshots of the beginning of transcription have revealed many other interactions that help explain the biology and open the door to structure-based drug design. But there are challenges ahead. The PIC is dynamic, forming and then breaking apart. And some vital questions remain about how the transcription process works from start to finish.

One key question for researchers is how the PIC proteins are expressed and then assemble before making the final complex. With so many components, researchers say, it seems sensible that groups of proteins form substructures and smaller complexes first. But the exact order of how these and the larger complex assemble is still unknown. Others want to know what happens after initiation, as transcription proceeds and the polymerase completes it work. But the level of detail already revealed is breathtaking, researchers say.

After 2 decades, researchers can see the details of how transcription starts. And these papers show that with the right structural biology expertise, other huge, flexible complexes are also within reach. “Ten, 20 years ago we were talking about this, but it was sort of like Star Trek,” Taatjes says. “Now all of a sudden, boom, there it is . . . and now the whole field realizes, ‘Wow, OK, we can do anything.’ ”

Another challenge is understanding and visualizing the dynamic processes that these complicated assemblies perform while in cells. At some point, Cramer says, it will be time for structural biology to pass the baton to other disciplines, such as microscopists. Maybe one day we can look forward to seeing videos of transcription happening inside cells.


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